title: PANC-1 cells, IKE treated, bioreplicate 4

data_processing:
Sequencing reads from RNA-seq were first filtered by fastp (version 0.18.0) to remove contaminating and low-quality reads, and then filtered using the short reads alignment tool Bowtie2 (version 2.2.8) to further remove reads that were mapped to ribosome RNA (rRNA) database.
The clean reads were then aligned to the reference genome (GRCh38) using HISAT2 (version 2.1.0). Stringtie (version 1.3.4) was applied for the reconstruction of transcripts, which were annotated using the KEGG and GO database.
Transcripts abundances were quantified using software StringTie by calculating the FPKM values.
Differential expression analysis was performed using DESeq2 software
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes FPKM values of each sample

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
rRNAs were removed from isolated total RNAs to retain mRNAs and ncRNAs, which were subsequently fragmented into short fragments and reverse transcribed into complementary DNA (cDNA) with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTPs and reaction buffer, after which the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis and PCR amplified.

value: 1 microM IKE,24 h


title: RDD 7SK Rep1

status: Public on May 21 2024

type: SRA

city: Shenzhen

first: Tian

last: (Simon) Zhongyuan

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

country: China

institute: Southern University of Science and Technology (SUSTech)

library_source: genomic

data_processing:
RDD: We processed RDD data using modified ChIA-PIPE pipeline. It includes the following main procedures: linker filtering, data alignment and qualification, coverage generation, interaction clustering, quality control, and finally data classification for visualization and further analyzation. Briefly, a configuration file and two FASTQ files (R1 reads and R2 reads) were taken. Firstly, read pairs are scanned for the RDD-linker sequence and partitioned into categories: read pairs with (i) no linker, (ii) one linker and one usable genomic tag, or (iii) a linker and PETs. PETs are aligned to a dm3 reference genome. The analysis-ready BAM file contains uniquely mapped, nonredundant PETs. Secondly, 2D chromatin interaction maps are generated using standardized file formats. Thirdly, using interligation PETs (span ≥ 3 kb), loops are called and then annotated with peak support. Then, the binding peaks of the RNA of interest are identified using SPP or MACS2. The 2D chromatin interaction maps can be viewed in Juicebox.js. The loop file, peak file, coverage file, and domain file can be viewed in BASIC Browser.
ChIA-PET:Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 using bwa-mem and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using Picard. Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
RNA-seq:the RNA-seq data was processed using STAR and RSEM. Firstly, the raw FASTQ files with pair-end reads were mapped to dm3 genome using STAR with ENCODE standard options. Secondly, FPKM of genes were calculated by utilizing ‘rsem-calculate-expression’ script of RSEM, with key configurations of ‘--paired-end’ and ‘--forward-prob 0’ for selecting reads that derived from the reverse strand. Then the uniquely mapped reads of total RNA-seq were hit and plotted the RPKM as boxplots.
Assembly: dm3
Supplementary files format and content: cluster, hic, bedgraph, peak
Library strategy: RDD

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured in Gibco™ Schneider’s Drosophila Medium supplemented with 10% fetal bovine serum  and maintained at 27 °C.

extract_protocol:
Dual-crosslinked cells were subjected for cell lysis and nuclei lysis. The lysed nuclei are fragmented into smaller complexes by sonication. Then the ncRNA of interest and its associated complexes are purified by hybridization using biotinylated antisense probes of a target ncRNA. And the purified complexes are immobilized on streptavidin C1 beads via high affinity with biotin, the excess unbound sites of beads are specifically blocked with denatured biotins to avoid the adsorption of biotinylated bridge-linker by streptavidin beads in later procedure of proximity ligation. Chromatin DNA contacts of complexes on beads are captured by incorporated biotinylated linkers between DNA sites during proximity ligation. Finally the ligated products are subjected for Tn5 tagmentation and enriched by streptavidin M280 beads for sequencing to obtain the specific RNA associated chromatin DNA–DNA interactions.
The ligated DNA was fragmented by using Tn5 transposase. Then the fragmented DNA contained RDD-linker were captured with Streptavidin beads and used for PCR amplification. These PCR products were then performed double size-selection with AMPure beads to achieve the DNA fragments with size of 300-600 bp, then subjected for Illumina NovaSeq 6000 with paired-end sequencing at read lengths of 150 bp.

treatment_protocol: For heat treatment, the exponential growth phase of cells were aliquot to three tubes, one tube was carried out crosslinking directly (Control, Ctrl), two tubes were subjected to 37 °C for 20 min and then one of them was stepped into crosslinking procedure immediately (heat shock, HS), the other was kept at room temperature for 20 min then was performed crosslinking (Recovery, RC).

tag: treatment

value: Wild type

tag: cell line

tag: cell type

value: late stage 20-24 hours old Drosophila melanogaster embryos

tag: enriched factor


title: Stage_III_Steady_State_2

city: Liege

first: Christophe

middle: J

last: Desmet

address: B34, Avenue de l'Hopital 1

country: Belgium

institute: University of Liege

library_source: transcriptomic

data_processing:
Sequenced reads were aligned and mapped to the mouse genome (mm10) with RNA-Seq Alignment (Version:2.0.2) using STAR_2.6.1a on BaseSpace (https://basespace.illumina.com).
Normalization and analysis of the obtained data was performed using DESeq2 R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: mm10
Supplementary files format and content: Tab-delimited file describing the number of reads mapped to each gene as obtained with RNA-Seq Alignment (Version:2.0.2) on BaseSpace (https://basespace.illumina.com).

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
For every mL of TRIzol, 200uL of chloroform was added, and the samples were vigorously mixed and incubated for 2 minutes at room temperature. Samples were centrifuged at 10,000xg for 15 minutes at 4°C to separate the phases. The RNA-containing upper aqueous phase was transferred to a new microcentrifuge tube containing 475uL of isopropanol and 2uL of glycoblue (ThermoFisher, AM9515). Samples were centrifuged at 10,000xg for 15 minutes and supernatant was discarded. One volume of 75% ethanol was added and samples were centrifuged at 10,000xg for 1 minute to precipitate the RNA and discard the supernatant. RNA pellet was resuspended in 40uL of DNase/RNase-free water for a 15-minute DNase treatment (Zymo Research, E1010). DNase treatment was followed by column-based RNA purification with the RNA Clean & concentrator-5 kit (Zymo Research, R1016). Briefly, 100uL of RNA binding buffer was added to every 50L sample and mixed thoroughly. One volume of 100% ethanol was added and the sample was transferred into a Zymo-Spin IC column in a collection tube. Columns were centrifuged at 10,000xg for 30 seconds and flow-through was discarded. The column was washed once with RNA prep buffer and twice with RNA wash buffer, following the manufacturer’s instructions. RNA was eluted in 10uL of DNase/RNase-free water. Purified RNA integrity and quantity was assessed using the RNA 6000 Pico kit (Agilent) for the presence of 18s and 28s rRNA peaks.
Full length cDNA was prepared from isolated RNA using SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio, 634889) following the manufacturer's instructions, with 17 cycles of cDNA amplification. Final cDNA quality was assessed using Agilent High Sensitivity DNA kit (Agilent, 5067-4626). cDNA libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina, FC-131-1024) using the manufacturer’s instructions.

treatment_protocol: Single cell suspensions of murine bone marrow were pooled from 3 CB57BL/6 donor mice in the steady state or from 3 mice that received daily intraperitoneal injections of 400 ng recombinant murine IL-33 for 7 days were first stained for Ly6G-FITC (BioLegend, 127606), CD90.2-FITC (BioLegend, 140204), NK1.1-FITC (eBioscience, 11-5941-85), CD45R-FITC (eBioscience, 11-0452-85) for 30 minutes on ice. Samples were immunomagnetically enriched for cells of interest using EasySep™ FITC positive selection kit II (Stemcell, 17682) as described by the manufacturer’s instructions. The negative fractions were subsequently stained for CD29-pacblue (BioLegend, 102224), F4/80-BV510 (BioLegend, 123125), Siglec-F-BV711(BD Biosciences,740764), CD55-biotin-streptavidin-BV786(R&D, BAF5376, BD Biosciences, 563858), CD117-BB700 (BD Biosciences, 566414), Pir-A/B-PE (BioLegend, 144104) and CD200R3-PE-cy7 (BioLegend, 142212) in 1X BD Horizon™ Brilliant stain buffer (BD Biosciences, 563794) for 30 minutes on ice. Cell suspensions were washed twice and resuspended in PBS supplemented with 5nM BD Via-Probe™ Green (BD Biosciences, 565802). cells in each of the four stages of eosinophil maturation were sorted directly into TRIzol (ThermoFisher, 15596026) using a BD FACSAria III (BD Biosciences) cell sorter with a 100μm nozzle. Sort purity was at 95 per cent or higher and samples were stored at -80°C for downstream RNA applications.

tag: tissue

value: Bone Marrow

tag: strain

value: Bone marrow eosinophil developmental stages

tag: genotype

value: wild type

value: steady state


title: PANC-1 cells, IKE treated, bioreplicate 3

city: Beijing

first: Dan

last: Su

address: No. 1 Shuaifuyuan, Wangfujing Street, Beijing

department: Department of General Surgery

institute: Peking Union Medical college hospital

organism: Homo sapiens

growth_protocol: PDAC cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM, Viacell),  or Iscove's Modified Dulbecco's Medium (IMDM, Viacell), which were supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% normocin (Invivogen), at 37 °C in a humidified incubator containing 5% CO2

treatment_protocol: CFPAC-1 and PANC-1 cells were treated with 10 μM or 1 μM  IKE (imidazole ketone erastin, a derivative of erastin) for 24 h. PDAC cells treated with 0.1% DMSO were used as a parallel control.  After removing dead cells and cell debris, survived PDAC cells were collected for sequencing analysis.

value: pancreatic adenocarcinoma cells


title: Donor4_Stimulated_ATM-inhibitor_Day3

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description:
150-bp paired end seq
104295-001-009

data_processing:
FastQC v0.11.9 was used to check raw reads, and Cutadapt v2.10 to perform adapter clipping.
Reads are mapped to a reference genome (Ensembl gene annotation v102, GRCh38) using STAR aligner v2.7.5a.
After removing PCR duplicates detected by UMI with umitools v0.5.5, HTSeq Count v0.12.4 was used for counting of aligned reads.
Assembly: GRCh38
Supplementary files format and content: TSV, gene count table

source_name: Sorted B-cells from healthy control

growth_protocol: Blood PBMC's were isolated using ficoll density gradient centrifugation, subsequently thawed and FACS sorted for naïve B-cells (CD20+CD27-IgG-IgA-)

extract_protocol:
GenElute Mammalian Total RNA kit (Sigma-Aldrich) or RNeasy Micro Kit (Qiagen)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), performed by GenomeScan B.V.

treatment_protocol: 3 to 6 day culture in medium containing IL10, IL21, anti-IgM and CD40L, with or without either ATM-inhibitor or DNA-PK-inhibitor.

value: Cultured cells

value: Stimulated Naive B-cells

value: Healthy Control

value: ATM-inhibitor

tag: time point


title: Stage_II_Steady_State_2


title: PANC-1 cells, IKE treated, bioreplicate 2


title: Donor4_Stimulated_DNA-PKinhibitor_Day3

description:
150-bp paired end seq
104295-001-008

value: DNA-PKinhibitor


title: RDD roX2 HS saturated sequencing

value: Heat shock


title: PANC-1 cells, IKE treated, bioreplicate 1


title: RDD roX2 Rep3 saturated sequencing


title: Donor4_Stimulated_DMSO_vehicle_Day3

description:
150-bp paired end seq
104295-001-007

value: DMSO


title: Donor3_Stimulated_ATM-inhibitor_Day3

description:
150-bp paired end seq
104295-001-006


title: Stage_I_Steady_State_2


title: RDD roX2 Rep2 deep sequencing


title: Stage_IV_Steady_State_1


title: PANC-1 cells, 0.1% DMSO treated, bioreplicate 1

value: 0.1percent DMSO,24 h


title: Stage_III_Steady_State_1


title: Donor1_Stimulated_ATM-inhibitor_Day6

description:
150-bp paired end seq
104295-001-012


title: RDD roX2 Rep1


title: CFPAC-1 cells, IKE treated, bioreplicate 2

value: 10 microM IKE,24 h


title: Stage_II_Steady_State_1


title: liver tissues from  the HBV-infected patients with cirrhosis 3

type: RNA

city: Xi'an

first: Chao

last: Fan

address: #169, Changle Road, Xincheng District

institute: The Fourth Military Medical University

description: Biological replicate 3 of 3. liver tissue from the HBV-infected patients with cirrhosis

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10 Blocking Agent and 1 μL of 25 Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2 Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 9samples were retained for further “m6A methylation level” and “m6A quantity” and “expression level”analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “RNA expression level” was calculatedbased on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities, and an additional quantile normalization method of limma package was used to normalize the RNA expression level between arrays before probes flag screening.Differentially m6A-methylated RNAs or expressed between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: liver tissue

label_protocol: The total RNAs were immunoprecipitatedwith anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactionsusing Arraystar Super RNA Labeling Kit. Reagents:Affinity purified anti-m6A rabbit polyclonal antibody (Synaptic Systems, 202003);DynabeadsTM M-280 Sheep Anti-Rabbit IgG (Invitrogen, 11203D);RNase inhibitor (Enzymatics, Y9240L)

growth_protocol: The liver tissues of a 3mm×3mm from different donors were collected during normal surgical operation associated with their symptomatic treatment. And the samples were kept at 4 °C.

extract_protocol: The total RNA were extracted by TRIzol reagent (CWbio, China), using the standard protocol for trizol extract. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No specific treatment was performed.

tag: donor sex

value: male

tag: donor age


title: Donor1_Stimulated_ATM-inhibitor_Day3

description:
150-bp paired end seq
104295-001-003


title: CFPAC-1 cells, IKE treated, bioreplicate 1


title: liver tissues from  the HBV-infected patients with cirrhosis 2

description: Biological replicate 2 of 3. liver tissue from the HBV-infected patients with cirrhosis


title: Stage_I_Steady_State_1


title: RDD roX2 Rep2

value: Wild type


title: Donor1_Stimulated_DNA-PKinhibitor_Day3

description:
150-bp paired end seq
104295-001-002


title: Steady state wild type bone marrow myeloid progenitors

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Myeloid progenitors (lineage-negative c-kit+ IL7Ra-) were sorted using a BD FACSAria III (BD Biosciences) cell sorter as described in Rosu et al.(DOI: 10.1084/jem.20200662 ) and were resuspended in Ca and Mg free PBS containing 0.4mg/ml of UltraPure™ BSA (Thermofisher, AM2616).In total, 16,000 sorted cells were submitted to the 10X Genomics pipeline for encapsulation aiming for a recovery of 10,000 sequenced single cells as described in the manufacturer’s instructions.
Sequencing libraries were prepared using Chromium Single Cell 3' Reagent Kit V3 (10X Genomics) as per manufacturer’s instructions and cDNA quality and quantity were controlled using Agilent High Sensitivity DNA Kit (Agilent) on a 2100 Bioanalyzer (Agilent).

value: Myeloid progenitors


title: Donor3_Stimulated_DNA-PKinhibitor_Day3

description:
150-bp paired end seq
104295-001-005


title: CFPAC-1 cells, 0.1% DMSO treated, bioreplicate 2


title: CFPAC-1 cells, 0.1% DMSO treated, bioreplicate 1


title: liver tissues from  the HBV-infected patients with cirrhosis 1

description: Biological replicate 1 of 3. liver tissue from the HBV-infected patients with cirrhosis


title: Donor1_Stimulated_DMSO_vehicle_Day3

description:
150-bp paired end seq
104295-001-001


title: liver tissues from  the HBV-infected patients without cirrhosis 3

description: Biological replicate 3 of 3. liver tissue from the HBV-infected patients without cirrhosis


title: PANC-1 cells, 0.1% DMSO treated, bioreplicate 2


title: Day 0, IP, ONP, Replicate 5

city: Cambridge

first: William

middle: Jacob

last: Gammerdinger

state: MA

address: Massachusetts Hall

country: USA

institute: Harvard University

data_processing:
Transcripts were quantified by a quasi-alignment approach using Salmon (version 1.6.0)
Assembly: mm10
Supplementary files format and content: Cobined counts data containing data from each sample

molecule: polyA RNA

source_name: Optic Nerve Proper

growth_protocol: RNA was directly extracted from mouse retinal astrocytes from freshly ennucleated eyes

extract_protocol:
mRNA extraction was performed with oligo-dT beads and capturing poly(A) tails
cDNA library preparation was done with the Smart-Seq HT Ultra-low input RNA kit

treatment_protocol: RNA was isolated from untreated animals

value: Optic Nerve Proper

tag: batch


title: HrAgo1-associated small RNAs

city: Wageningen

first: Daan

middle: C.

last: Swarts

address: Stippeneng 4

department: Laboratory of Biochemistry

institute: Wageningen University

description:
HrAgo1_sRNA
Protein-nucleic acid complexes purified from E. coli, nucleic acids extracted, small RNA sequencing protocol

library_source: other

data_processing:
Paired-end small DNA reads were merged and adapter sequences were trimmed using BBmap (Bbtools v38.90; https://pubmed.ncbi.nlm.nih.gov/29073143/). Max length was set at 35 nucleotides
Reads were aligned against the genome of E. coli BL21(DE3) (CP053602.1) and protein expression plasmids (pFWC01) using HISAT2 v2.1.0 (https://pubmed.ncbi.nlm.nih.gov/25751142/)
Mapped reads were filtered using Samtools and analyzed using FastQC to determine read length and to investigate nucleotide bias
Aligned reads were analyzed using FeatureCounts to determine mapping frequence on genomic and plasmid features.
Assembly: Reads were aligned against the genome of E. coli BL21(DE3) (CP053602.1) and protein expression plasmid (pFWC01)
Supplementary files format and content: Analysis to which genome/plasmid reads map and fastqc read length and nucleotide bias analysis (sRNA_analyses.xlsx)
Supplementary files format and content: FeatureCounts analyses for each genome/plasmid present (FeatureCounts_results.xlsx)

molecule: other

organism: Escherichia coli

source_name: BL21-Gold (DE3)

growth_protocol: E.coli culture was inoculated into Terrific medium supplemented with 50 μg/ml Kanamycin and was shaken at 180 rpm at 37°C in an incubator until an OD600 nm of 0.4. IPTG was added to reach a final concentration of 0.1 mM, and the culture was moved to 24 °C and kept shaking for 8 hours. Cells were harvested by centrifugation at 4,250 x g at 4°C for 20 minutes

extract_protocol:
To extract nucleic acids co-puriﬁed with HrAgo1, 2 nmoles of purified protein was incubated with 250 µg/ml proteinaseK (Thermo Scientific) for 4h at 65C. Next, phenol:chloroform:IAA 25:24:1 pH 7.9 (Invitrogen) was added in a 1:1 ratio.  The sample was vortexed and centrifuged at 16000 x g in a table top centrifuge for 10 min. The  upper layer containing the nucleic acids was transferred to a clean tube and the nucleic acids were  precipitated through ethanol precipitation. To this end, 99% cold ethanol and 3 M sodium acetate  pH 5.2 were added to the sample in a 2:1 and 1:9 ratio, respectively. The sample was incubated  overnight at -80°C, after which it was centrifuged at 16000 x g in a table top centrifuge for 1 h. The  pellet was washed with 70% ethanol and subsequently dissolved in nuclease-free water.
The small RNAseq library was constructed by GenomeScan (Leiden, NL) using standard small RNA library preparation protocols

treatment_protocol: The pelleted cells were lysed by sonication (Daxluot Multichannel sonicator with 6mm tip, 5s ON/8 s OFF for 1 hour under constant cooling circulation) in Lysis Buffer (500mM NaCl, 5 mM Imidazole, 50 mM Tris-HCl pH 8) supplemented with 1mM PMSF and a protease inhibitor cocktail (Roche). TCEP was added immediately after sonication to a concentration of 1mM. After centrifugation at 6000 x g for 30 minutes at 4C, the cell-free extract was loaded on 5 ml HisTrap HP column (Cytiva Life Sciences) which was subsequently washed with Washing Buffer I (500 mM NaCl, 20 mM Imidazole, 1mM TCEP, 50 mM Tris-HCl pH 8). Bound protein was eluted with 15 ml Elution Buffer (500 M NaCl, 500 mM Imidazole, 5% glycerol, 50 mM Tri-HCl pH 8). The sample was concentrated to a volume of 2 ml using 30kDa Amicon ultracentrifugal filter. Imidazole-free buffer (500 M NaCl, 5% glycerol, 50 mM Tri-HCl pH 8) was added, well-mixed and re-concentrated three times to replace the original buffer. The final round of centrifugation was done to result in approximately 1ml solution, moved to a fresh 1.5 ml tube and was centrifuged for 30 min at 16,000 x g at 4C to remove aggregates. The supernatant was loaded on a Superdex 200 Increase 10/300 GL column (Cytiva) for size exclusion. The peak fractions were analyzed by SDS-PAGE and fractions containing HrAgo1 were combined and concentrated, aliquoted and flash frozen in liquid nitrogen before storage at -80C until further use.

value: BL21-Gold (DE3)

value: No treatment


title: liver tissues from  the HBV-infected patients without cirrhosis 2

description: Biological replicate 2 of 3. liver tissue from the HBV-infected patients without cirrhosis

value: female


title: IL-33-ILC2 KO-3

city: Shanghai

first: Hongshen

last: Niu

state: Shanghai

address: south chongqing road 280

department: shanghai institute of immunology

institute: Shanghai jiao tong university school of medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were aligned to the mouse reference genome (version mm10) by using Hisat2 RNASeq alignment software.
Quantitated relative mRNA expression levels (FPKM) were calculated based on exon regions using Cufflinks and the mm10 reference genome annotations.
Assembly: mm10
Supplementary files format and content: comma-separated values files include readcounts (column J-M) and FPKM values (column N-Q) for each Sample and every gene

source_name: Lung

extract_protocol:
Total RNA from sorted lung ILC2s of R5/+ (WT) and R5/+ LKB1f/f (KO) mice treated with IL-33 or not  was extracted by Trizol reagent. Each sample was a pool of 3-4 mice. RNA quality was examined with an Agilent Bioanalyzer 2100 (Agilent). The concentration of RNA was from 7ng/ul to 14ng/ul. The SMART-Seq HT Kit (Takara Bio USA, Inc) was used to generate high-quality, full-length cDNA.
Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol.

value: Lung

value: 4 days of IL-33 challenge


title: PXB Liver, HBV Infected + Vehicle, Day 42 rep 2

city: Foster City

first: Cameron

last: Soulette

address: 333 Lakeside Dr

institute: Gilead Sciences

description:
Humanized Mouse
rp102_inf_veh
upa-scid_rawcounts.csv

data_processing:
Gene counts files were generated.
Assembly: Hg38 & mm10
Supplementary files format and content: csv, gene counts

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
polyA
Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103)
HiSeq-Sequencing-2x50bp-PE sequencing on an Illumina sequencing platform
Briefly, Total RNA samples are concentration normalized, and polyadenylated RNA is purified using oligo-dT attached to magnetic beads. Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix. A single ‘A’ base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information. Final libraries are quantified, normalized and pooled. Pooled libraries are bound to the surface of a flow cell and each bound template molecule is clonally amplified up to 1000-fold to create in- dividual clusters. Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain. Each nucleotide label acts as a terminator for polymerization, thereby en- suring that a single base is added to each nascent chain during each cycle. Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

value: Liver

tag: group

value: PXB Liver

value: HBV Infected + Vehicle, Day 42


title: D23580_C1_Rep1

city: Tempe

first: Jiseon

last: Yang

state: AZ

address: 1001 S. McAllister Ave

institute: Arizona State University

description: FS4; Barcode: CAGATC

data_processing:
A series of quality control metrics were generated on the STAR outputs. Stringtie-1.3.4c was used to report read counts, FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million). RNA-Seq reads for each sample were quality checked using FastQC v0.10.1, aligned to the S. Typhimurium D23580 chromosome FN424405 and plasmid pST-BT FN432031, counted per gene, and quantified as FPKM values and TPM by TopHat and Cufflinks software. When data from duplicated samples for each group were merged, we detected an average of ~2,500 genes (out of ~4,500 protein coding genes in the genome) with FPKM > 1 with average coverage of ~50x.
Differential expression (DE) analysis was performed with EdgeR package from Bioconductor v3.2 in R 3.2.3. EdgeR applied an overdispersed Poisson model to account for variance among biological replicates. Empirical bayes tagwise dispersions are also estimated to moderate the overdispersion across transcripts. Then a negative bionomial generalized log-linear model was fit to the read counts for each gene for all comparison pairs.
For each pairwise comparison, genes with false discovery rate (FDR) <0.05 were considered significant and log2-fold changes of expression between conditions (logFC) were reported. False discovery rate (FDR) was also calculated following Benjamini & Hochberg (1995) procedure.
Pathway enrichment was performed by DAVID 6.8 Functional Annotation Tool
Differentially regulated transcripts were analyzed for enrichment in GO terms and KEGG pathways using a threshold count of 2, an EASE score of 0.05 and Benjamini-Hochberg correction (< 0.05).
Assembly: aligned to the S. Typhimurium D23580 chromosome FN424405 and plasmid pST-BT FN432031
Supplementary files format and content: text file containing Edge R read counts

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

source_name: Bacterium

growth_protocol: S. Typhimurium ST313 strain D23580 was cultured in Lennox broth (LB) at 37°C for all experiments. An overnight culture of D23580 grown for 15-16 h with aeration was diluted 1:200 into fresh LB and loaded into the RWV bioreactors with or without beads. Bacterial cells were grown for 24 hours to stationary phase.

extract_protocol:
Bacterial cells were fixed with RNAlater. Total RNA was purified using the miRNeasy kit (Qiagen) and quantified using a Nanodrop spectrophotometer, and the integrity verified by formaldehyde-agarose gel electrophoresis.
Sample cDNA libraries were generated utilizing the Encore complete prokaryotic RNA-Seq library systems. The barcodes used for RNA-Seq are listed in Supplementary Table 1. The synthesized cDNAs (generated with Nugen’s Ovation SPIA chemistry) were fragmented, ligated with adaptors using Kapa Biosystems NGS library preparation kit, and PCR-amplified using Kapa Biosystems HiFi polymerase to generate sequencing libraries. Six-plexed 2x100 bp paired-end sequencing yielded a total of 202 million pairs of reads, and the reads per sample ranged from 28 to 48 million.

treatment_protocol: Beads of differing size and density were used to generate a range of incrementally increasing fluid shear levels in the RWV: 1/8” (3.175 mm) diameter polypropylene (1/8-PP); and 1/8” diameter ceramic (1/8-C) (Baltec, Inc., Los Angeles, CA.).  The RWV without beads generates a low fluid shear environment with less than 0.01 dynes/cm2, while the addition of  a 1/8-PP bead or a 1/8-C bead generates 7.8 dynes/cm2 or 14 dynes/cm2, respectively.

value: Bacterium

value: wt

value: ceramic bead


title: Donor3_Stimulated_DMSO_vehicle_Day3

description:
150-bp paired end seq
104295-001-004

value: Cultured cells

value: Stimulated Naive B-cells

value: Healthy Control

value: DMSO


title: PXB Liver, HBV Infected + Vehicle, Day 42 rep 3

description:
Humanized Mouse
rp103_inf_veh
upa-scid_rawcounts.csv


title: D23580_C2_Rep2

description: FS4; Barcode: CTTGTA


title: IL-33-ILC2 KO-2


title: liver tissues from  the HBV-infected patients without cirrhosis 1

description: Biological replicate 1 of 3. liver tissue from the HBV-infected patients without cirrhosis

value: male


title: PXB Liver, HBV Infected + Vehicle, Day 42 rep 1

description:
Humanized Mouse
rp101_inf_veh
upa-scid_rawcounts.csv


title: D23580_PP2_Rep2

description: FS3; Barcode: GCCAAT

value: Polypropylene bead


title: IL-33-ILC2 KO-1


title: liver tissues from the healthy donors 3

description: Biological replicate 3 of 3. liver tissue from the healthy donor.


title: D23580_PP1_Rep1

description: FS3; Barcode: ACAGTG


title: PXB Liver, HBV Infected + Treatment, Day 42 rep 3

description:
Humanized Mouse
rp403_inf_trt
upa-scid_rawcounts.csv

value: HBV Infected + Treatment, Day 42


title: liver tissues from the healthy donors 2

description: Biological replicate 2 of 3. liver tissue from the healthy donor.


title: D23580_N2_Rep2

description: FS1; Barcode: TGACCA

value: no bead


title: IL-33-ILC2 WT-2


title: IL-33-ILC2 WT-3


title: liver tissues from the healthy donors 1

description: Biological replicate 1 of 3. liver tissue from the healthy donor.


title: PXB Liver, HBV Infected + Treatment, Day 42 rep 1

description:
Humanized Mouse
rp401_inf_trt
upa-scid_rawcounts.csv


title: D23580_N1_Rep1

description: FS1; Barcode: CGATGT


title: S. rosetta cell-type transcriptomes:  Thecate, replicate 2

status: Public on May 20 2024

city: San Francisco

first: David

middle: S

last: Booth

state: CA

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
RNA libraries were sequenced at the QB3/UC-Berkeley Vincent J. Coates Genomic Sequencing Laboratory, and this laboratory demultiplexed the libraries using fastqc (v 0.11.9)
Assembly: Ensembl Protsits Salpingoeca rosetta str. ATCC 50818 (GCA_000188695.1)
Supplementary files format and content: csv file of TPM values genes in each sample. Transcripts were quantified using kallisto (PMID: 27043002) and sleuth  (PMID: 28581496).

organism: Salpingoeca rosetta

source_name: SrEpac HD1

extract_protocol:
10 million cells were lysed in 100 µl of preferential lysis buffer ( 20 mM Tris-HCl, pH 8.0; 150 mM KCl; 5 mM MgCl2; 250 mM sucrose; 1 mM DTT; 10 mM digitonin; 1 mg/ml sodium heparin; 1 mM Pefabloc SC; 100 mg/ml cycloheximide; 0.5 U/ml Turbo DNase; 1 U/ml SUPERaseIN). This was incubated on ice for 10 minutes, passed ten times through a 30G needle and centrifuged at 6,000 x g for 10 minutes at 4C. The supernatant was collected, brought to 100 µl with RNAse-free water, and RNA was purified using the RNAeasy kit from Qiagen (Cat. No. 74104), and eluted in 30 µl of water.
KAPA mRNA HyperPrep kit (KAPA biosystems, Cat. No. KK8580) according to manufacturer's instructions

value: SrEpac HD1

value: Thecate


title: S. rosetta cell-type transcriptomes:  Thecate, replicate 1


title: S. rosetta cell-type transcriptomes:  Fast Swimmer, replicate 3

source_name: SrEpac (ATCC PRA-390)

value: SrEpac (ATCC PRA-390)

value: Fast Swimmer


title: S. rosetta cell-type transcriptomes:  Fast Swimmer, replicate 2


title: S. rosetta cell-type transcriptomes:  Fast Swimmer, replicate 1


title: S. rosetta cell-type transcriptomes:  Thecate, replicate 3


title: S. rosetta cell-type transcriptomes:  Rosette, replicate 3

value: Rosette


title: S. rosetta cell-type transcriptomes:  Rosette, replicate 2


title: S. rosetta cell-type transcriptomes: Slow Swimmer, replicate 2

value: Slow Swimmer


title: S. rosetta cell-type transcriptomes: Slow Swimmer, replicate 3


title: S. rosetta cell-type transcriptomes:  Rosette, replicate 1


title: S. rosetta cell-type transcriptomes: Slow Swimmer, replicate 1


title: sharpblue_rep1_WGBS

first: Zejia

last: Wang

address: Yanyuan Street

institute: Peking University

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to reference genome(2019 gigascience) using BSseeker2  under default. Reads with more than three consecutive methylated CHH were removed as described previously. CGmaptools is used for downstream analysis and visualization
V_corymbosum_v1.0
The processed data is generated  by BSseeker2 and Cgmaptools.
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
V_corymbosum_v1.0
The processed data is generated  by HISAT2

organism: Vaccinium corymbosum

source_name: leaf

extract_protocol: Blueberry leaves were collected for DNA extraction using a CTAB-based method. 400 ng DNA was used for bisulfite conversion with the EZ DNA methylation-lighting kit

value: leaf

value: wild type

tag: time

value: after flowering


title: draper_rep2_WGBS


title: sharpblue_rep2_WGBS


title: draper_rep3_RNAseq

data_processing:
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
V_corymbosum_v1.0
The processed data is generated  by HISAT2
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
V_corymbosum_v1.0
The processed data is generated  by HISAT2

extract_protocol: The total RNA was isolated from the strain using the Trizol reagent according to manufacturer’s instructions (Invitrogen) and sent to Novogene (Tianjin, China) for library  preparation and deep sequencing.


title: draper_rep1_RNAseq


title: draper_rep1_WGBS


title: PXB Liver, HBV Infected + Treatment, Day 42 rep 2

description:
Humanized Mouse
rp402_inf_trt
upa-scid_rawcounts.csv

value: Liver

value: PXB Liver


title: sharpblue_rep3_RNAseq


title: draper_rep2_RNAseq


title: sharpblue_rep2_RNAseq


title: sharpblue_rep1_RNAseq


title: X10_WGBS

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to reference genome(2019 gigascience) using BSseeker2  under default. Reads with more than three consecutive methylated CHH were removed as described previously. CGmaptools is used for downstream analysis and visualization
Assembly: V_corymbosum_v1.0
Supplementary files format and content: generated  by BSseeker2 and Cgmaptools.

value: no


title: IL-33-ILC2 WT-1

value: Lung

value: 4 days of IL-33 challenge


title: X3_WGBS


title: S79_WGBS


title: S76_WGBS


title: S70_WGBS


title: S58_WGBS


title: S56_WGBS


title: S53_WGBS


title: S59_WGBS


title: S55_WGBS


title: S43_WGBS


title: S26_WGBS


title: S45_WGBS


title: 24-day-old male offspring of dams with fatty liver: deprived with choline during pregnancy and lactation 2

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from LnCap cell line

hyb_protocol: The biotin-labeled cDNA was hybridized (Affymetrix® Rat Gene 2.1 ST Array Strip) and stained by Affymetrix GeneAtlas Fluidcs Station of GeneAtlas System. Obtained data were visualized by the Imaging Station of the GeneAtlas System (Affymetrix, Santa Clara, CA, USA) and analyzed by GeneAtlas Operating System (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

organism: Rattus norvegicus

source_name: liver from 24-day-old male Wistar rats

label_protocol: Synthesis of cDNA was carried out from total RNA (100 ng) by a two-step PCR reaction (biotin labeling and fragmentation), according to the manufacturer’s protocol (GeneChip® WT Plus Reagent Kit, Affymetrix, Santa Clara, CA, USA).

growth_protocol: Thirty-four animals were included in the study: seventeen dams and seventeen male offspring. Eighteen female and nine male rats eight weeks old were obtained from Charles River Laboratories (Germany). Animals were housed at the Laboratory of the Department of Human Nutrition and Dietetics, Poznań University of Life Sciences under standard conditions (12/12 h light/dark cycle, 21 ± 1 °C, humidity 55 %–65 %,) and were kept in pairs/in threes within the same sex in stainless steel cages coated with metal-free enamel.

extract_protocol: Total RNA was isolated from rat liver by using TRIzolTM Reagent according to procedure (Thermo Fisher Scientific; Waltham; MA; USA). The quality and quantity of RNA have been analyzed spectrophotometrically (DS-11; Wilmington, DE; USA) and each RNA sample has been diluted by nuclease-free water (Thermo Fisher Scientific; Waltham; MA; USA) for final RNA concentration of 100 ng/ul.

treatment_protocol: After a five-day adaptation period, when animals have been fed standard maintenance diet Labofeed B (Morawski, Poland), females started to be fed with the AIN-93 M diet deficient in choline (D group, n=17, one dam was excluded from the study because of malocclusion) (Reeves et al., 1993) for 16 weeks to establish a fatty liver model (Veteläinen et al., 2007). Next, dams were mated with healthy Wistar males fed with the standard AIN-93 M diet. A vaginal plug was the evidence of mating. Pregnant dams with fatty liver were randomized to two subgroups: one was still fed the diet deficient in choline (D group, n=9); the second one started to receive proper choline amounts in the diet (standard AIN-93 G diet; N group, n=8). Three days before expected delivery, dams started to be kept in a single cage. After delivery, the animals from the D group were randomized once again into two subgroups, which were still fed the diets deficient in choline (DD group, n=4) or with the standard AIN-93 G diet (DN group, n=5). The same was done with animals from the N group – one subgroup was still fed standard AIN-93 G diet (NN group, n=4) and the second started to be fed diet deficient in choline (ND group, n=4). This feeding method in the DD, DN, ND and NN groups were continued till 24. day after delivery, when one male from each litter was sacrificed for tissue collection.

value: liver

tag: age

tag: Sex

value: male

value: Wistar


title: 24-day-old male offspring of dams with fatty liver: deprived with choline during pregnancy and lactation 4


title: 24-day-old male offspring of dams with fatty liver: deprived with choline during pregnancy and lactation 3


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during pregnancy 3


title: H41_WGBS


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during lactation 4


title: H46_WGBS


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during lactation 3


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during pregnancy 4


title: H43_WGBS


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during pregnancy 5


title: 24-day-old male offspring of dams with fatty liver: provided with proper choline amount during pregnancy and lactation 4


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during lactation 1


title: 24-day-old male offspring of dams with fatty liver: deprived with choline during pregnancy and lactation 1


title: H40_WGBS


title: genomic DNA from DLBCL.nonGC sample 96

type: genomic

city: Umeå

first: Magnus

last: Hultdin

state: Vasterbotten

address: 6M-building, NUS, 2d floor

department: Department of Medical Biosciences, Pathology

country: Sweden

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
The Genome Studio software V2011.1 (Illumina) and the R statistical software, version 4.2.2. (R core team)
Beta values

label: Cy5 and Cy3

source_name: DLBCL.nonGC sample 96

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA mini kit (#80204, Qiagen, Hilden, GER) according to the manufacturer’s instructions

tag: entity


title: genomic DNA from normal GC B-cells

source_name: normal GC B-cells

value: Normal germinal center B-cells from tonsil


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during pregnancy 2


title: genomic DNA from DLBCL.GC sample 95

source_name: DLBCL.GC sample 95


title: H33_WGBS


title: 24-day-old male offspring of dams with fatty liver: provided with proper choline amount during pregnancy and lactation 1


title: H35_WGBS


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during pregnancy 1


title: genomic DNA from t.DLBCL sample 93

source_name: t.DLBCL sample 93


title: H13_WGBS


title: 24-day-old male offspring of dams with fatty liver: provided with proper choline amount during pregnancy and lactation 2


title: 48h Induced iSLK-WTBAC

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 1200 Newell Dr.

institute: University of Florida

data_processing:
Merged the fastq files that were assigned "passed.fastq".
Aligned of the fastq file to KSHV genome (NCBI accession number NC_009333.1) using minimap2
Generated gtf files from KSHV aligned bam files to identify transcript structures in both default and flipped (anti-sense) orientations
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Transcript structures in gtf format
Library strategy: PCR-cDNA Sequencing

source_name: iSLK

growth_protocol: Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in DMEM plus 10% fetal bovine serum, 1% Penicillin-Streptomycin, 1 μg/ml puromycin, 250 μg/ml G418 and 250 μg/ml hygromycin

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol.
Poly(A)-tailed RNA was selected from 75 μg of each RNA sample using Dyna Beads mRNA purification kit (Invitrogen, Catalog No. 61006). PCR-cDNA sequencing libraries were prepared by using SQK-PCB109 (ONT) library preparation kit with 1 ng of each polyA-selected RNA sample.

treatment_protocol: Induction with Doxorubicin (1 ug/ml) and sodium butyrate (1 mM).

value: iSLK

value: Endothelial Cells

value: WT

value: 48h Induced


title: genomic DNA from t.DLBCL sample 91

source_name: t.DLBCL sample 91


title: 24h Induced iSLK-WTBAC

value: 24h Induced


title: 24-day-old male offspring of dams with fatty liver: deprived with choline only during lactation 2


title: genomic DNA from t.DLBCL sample 90

source_name: t.DLBCL sample 90


title: Sample Stop50_2

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Reads were trimmed for adapters and low-quality bases using the Cutadapt v1.18.
Reads were aligned to our hybrid genome (mm10_MHV68YFP_Krug.fa) using STAR v2.4.2a in 2-pass mode.
Gene and isoform expression was quantified using RSEM v1.3.3 with our custom GTFs (see below)..
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by differential expression of genes analysis.
To map both host and viral reads, the viral genome was added as an extra chromosome to the mm10 genome, and the viral GTFs appended to the M21 mouse gene annotation (see provided FA and GTF files).
Assembly: The host genome was mm10 using the M21 annotation, while our custom viral genome consisted of MHV68 with our YFP inserted into it. Two GTFs for the viral genome were created, one with full ORF annotaions (Krug_Ov) and one where overlapping sections were removed (Krug_NoOv). The data were analyzed with both GTFs for comparison.
Supplementary files format and content: The FASTA (.fa) file provided contains our hybrid genome consisting of the mm10 mouse genome concatenated to our viral genome represaented as its own chromosome, which is MHV68 with our YFP marker inserted into it.
Supplementary files format and content: The GTF (.gtf) files provided are for our Non-Overlapping (Krug_NoOv) gene annotation (where ORFs are trimmed to remove overlapping regions to make conservative expression estimates) and Overlapping (Krug_Ov) gene annotation, with full-length ORFs.
Supplementary files format and content: The TXT (.txt) files provided are RSEM CPM TMM counts for the expression of our samples aligned against our hybrid genomes (Krug_NoOv and Krug_Ov).

organism:
Mus musculus
Murid gammaherpesvirus 4

source_name: cell line

growth_protocol: NIH 3T12 (ATCC CCL-164) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 ug/ml penicillin, 100 ug/ml streptomycin, and 2 mM L-glutamine to form complete DMEM (cDMEM).

extract_protocol:
Total RNA was extracted using Trizol following manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).
Stranded, Poly A selection.

treatment_protocol: NIH 3T12 fibroblasts were infected with ORF50.stop or WT MHV68 at MOI 3 for 18 hours.

value: cell line

value: NIH 3T12

value: fibroblast

value: MHV68 ORF50.stop


title: Sample Stop50_3


title: genomic DNA from t.DLBCL sample 89

source_name: t.DLBCL sample 89


title: genomic DNA from t.DLBCL sample 86

source_name: t.DLBCL sample 86


title: 48h Induced BCBL-1

data_processing:
Merged the fastq files that were assigned "passed.fastq" by the minKnow software.
Aligned of the fastq file to KSHV genome (NCBI accession number NC_009333.1) using minimap2
Generated gtf files from KSHV aligned bam files to identify transcript structures in both default and flipped (anti-sense) orientations
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Transcript structures in gtf format
Library strategy: direct-cDNA Sequencing

growth_protocol: Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol.
Poly(A)-tailed RNA was selected from 75 μg of each RNA sample using Dyna Beads mRNA purification kit (Invitrogen, Catalog No. 61006). Direct-cDNA sequencing libraries were prepared by using SQK-DCS109 (ONT) library preparation kit with 100 ng of each polyA-selected RNA sample.

treatment_protocol: Induction with 12-O-tetradecanoylphorbol-13-acetate (TPA) (20 ng/ml) and sodium butyrate (2 mM) for 48 h

value: Primary effusion lymphoma cells

value: Induced


title: genomic DNA from t.DLBCL sample 84

source_name: t.DLBCL sample 84


title: genomic DNA from DLBCL.GC sample 94

source_name: DLBCL.GC sample 94


title: genomic DNA from t.DLBCL sample 87

source_name: t.DLBCL sample 87


title: 24h Induced BCBL-1


title: genomic DNA from t.DLBCL sample 85

source_name: t.DLBCL sample 85


title: Sample Stop50_1


title: 24-day-old male offspring of dams with fatty liver: provided with proper choline amount during pregnancy and lactation 3


title: genomic DNA from t.DLBCL sample 83

source_name: t.DLBCL sample 83


title: Sample MR_3

value: MHV68 WT


title: genomic DNA from t.DLBCL sample 82

source_name: t.DLBCL sample 82


title: genomic DNA from t.DLBCL sample 92

source_name: t.DLBCL sample 92


title: genomic DNA from PCNSL sample 80

source_name: PCNSL sample 80

value: PCNSL


title: H9_WGBS

source_name: leaf

value: leaf

value: wild type

value: no

value: after flowering


title: Sample MR_1


title: genomic DNA from PCNSL sample 81

source_name: PCNSL sample 81


title: Uninduced BCBL-1

value: Uninduced


title: Uninduced iSLK-WTBAC

value: iSLK

value: Endothelial Cells


title: genomic DNA from PCNSL sample 78

source_name: PCNSL sample 78


title: SP4_OTII-ctl_neg_rep2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each gene

source_name: thymus

growth_protocol: Mixed radiation bone marrow chimeras were created using wild-type and RIP-mOVA hosts to model positive and negative selection (i.e. clonal deletion), respectively. Lethally irradiated host mice were reconstituted with a competitive mix of bone marrow from three congenically marked donors: OTII Nr4a1-/- Nr4a3-/- double knock-out (OTII-DKO), control OTII Nr4a1+/+ Nr4a3+/+ (OTII-ctl), and non-transgenic wild-type at an input ratio of 1:1:3, respectively. Roughly five weeks after irradiation and bone marrow transfer, post-selection immature single positive OTII-ctl and OTII-DKO thymocytes (differentiated by congenic marker) were sorted from both host types based on surface marker expression: CD4+ CD8- CD69+ Vα2+ Vβ5+. In this model, both OTII-ctl and OTII-DKO cells are positively selected in WT hosts. In RIP-mOVA hosts, OTII-ctl thymocytes undergo marked deletion by the SP4 stage, while OTII-DKO thymocytes escape deletion. Of note, in both host types the Treg compartment derives primarily from the non-transgenic wild-type donor.

extract_protocol:
Cells were FACS sorted directly into RLT + 1%BME and snap frozen. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research).
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: thymus

value: CD4 single positive thymocyte

tag: sorting markers

value: CD4+ CD8- CD69+ Valpha2+ VBeta5+

tag: donor transgene

value: OT-II

tag: donor nr4a1_genotype

tag: donor nr4a3_genotype

tag: donor _background

value: B6.Cg-Tg(TcraTcrb)425Cbn/J  x BoyJ (F1)

tag: host type

value: RIP-mOVA

tag: host background

value: C57BL/6-Tg(Ins2-TFRC/OVA)296Wehi/WehiJ x BoyJ (F1)

tag: mouse

value: RIP-mOVA biol rep 2

tag: reconstituion time_(weeks)


title: 48h Induced BCBL-1

data_processing:
Merged the fastq files that were assigned "passed.fastq" by the minKnow software.
Aligned of the fastq file to KSHV genome (NCBI accession number NC_009333.1) using minimap2
Generated gtf files from KSHV aligned bam files to identify transcript structures
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Transcript structures in gtf format

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol.
Poly(A)-tailed RNA was selected from 75 μg of each RNA sample using Dyna Beads mRNA purification kit (Invitrogen, Catalog No. 61006). Direct-RNA sequencing libraries were prepared by using SQK-RNA002 (ONT) library preparation kit with 50 ng of each polyA-selected RNA sample.
direct-RNA Sequencing

tag: cell line

tag: cell type

value: Primary effusion lymphoma cells

tag: genotype

value: WT

tag: treatment

value: Induced


title: genomic DNA from PCNSL sample 77

source_name: PCNSL sample 77

value: PCNSL


title: SP4_OTII-DKO_neg_rep1

tag: tissue

value: RIP-mOVA biol rep 1


title: 24h Induced BCBL-1


title: genomic DNA from PCNSL sample 75

source_name: PCNSL sample 75


title: genomic DNA from PCNSL sample 74

source_name: PCNSL sample 74


title: genomic DNA from HGBL sample 73

source_name: HGBL sample 73

value: HGBL


title: SP4_OTII-ctl_neg_rep1


title: Sample MR_2

source_name: cell line

value: cell line

value: NIH 3T12

value: fibroblast

value: MHV68 WT


title: genomic DNA from HGBL sample 71

source_name: HGBL sample 71


title: SP4_OTII-DKO_pos_rep3

value: thymus

value: CD4 single positive thymocyte

value: wild-type

value: BoyJ

value: WT biol rep 3


title: cwf12_rep2

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Quality controls for fastq.gz files using fastq.gzC
Trim of low quality read bases from fastq.gz files as well as removal of adapters and other contaminants using Trimmomatic
Alignment againts the Schizosaccharomyces pombe ASM294v2  genone referenceusing STAR
Confirmation that no coverage biases are present in the aligned data according to genomic reference file using QualiMap2
Read count overlapping Schizosaccharomyces pombe ASM294v2 genomic features using htseq-count
Test for differentially expressed features between conditions using DESeq2
Assembly: Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: tab-separated .txt table of raw counts for all the samples

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: WT (972), saf5 and cwf12 strain were grown in YE5S media at 30ºC at OD600 of 0.5

extract_protocol:
Hot phenol extraction
TrueSeq Stranded mRNA sample Prep kit v2 following manufacterer's instructions

value: yeast

value: untreated


title: genomic DNA from PCNSL sample 79

source_name: PCNSL sample 79


title: SP4_OTII-DKO_neg_rep2

value: CD4+ CD8- CD69+ Valpha2+ VBeta5+

value: OT-II

value: RIP-mOVA

value: C57BL/6-Tg(Ins2-TFRC/OVA)296Wehi/WehiJ x BoyJ (F1)

value: RIP-mOVA biol rep 2


title: genomic DNA from HGBL sample 69

source_name: HGBL sample 69

value: HGBL


title: Uninduced BCBL-1

value: Primary effusion lymphoma cells

value: WT

value: Uninduced


title: SP4_OTII-ctl_pos_rep2

value: B6.Cg-Tg(TcraTcrb)425Cbn/J  x BoyJ (F1)

value: WT biol rep 2


title: genomic DNA from HGBL sample 70

source_name: HGBL sample 70


title: SP4_OTII-DKO_pos_rep2

value: thymus

value: CD4 single positive thymocyte


title: genomic DNA from HGBL sample 72

source_name: HGBL sample 72


title: genomic DNA from HGBL sample 68

source_name: HGBL sample 68


title: saf5_rep2


title: genomic DNA from HGBL sample 67

source_name: HGBL sample 67


title: genomic DNA from DLBCL.nonGC sample 66

source_name: DLBCL.nonGC sample 66


title: SP4_OTII-DKO_pos_rep1

value: wild-type

value: BoyJ

value: WT biol rep 1


title: genomic DNA from DLBCL.nonGC sample 65

source_name: DLBCL.nonGC sample 65


title: genomic DNA from PCNSL sample 76

source_name: PCNSL sample 76

value: PCNSL


title: saf5_rep1

value: yeast

value: untreated


title: SP4_OTII-ctl_pos_rep1

source_name: thymus

value: CD4+ CD8- CD69+ Valpha2+ VBeta5+

value: OT-II


title: genomic DNA from DLBCL.nonGC sample 64

source_name: DLBCL.nonGC sample 64


title: genomic DNA from DLBCL.nonGC sample 63

source_name: DLBCL.nonGC sample 63


title: genomic DNA from DLBCL.nonGC sample 62

source_name: DLBCL.nonGC sample 62


title: cwf12_rep1


title: AS3h6

first: Houyu

last: Zhao

state: Yangpu

address: No. 5, Panshan Road, Yangpu District, Shanghai

institute: Naval medical university

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.5 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
Clean reads were aligned to the Rat reference genome mRatBN7.2 using STAR.
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM raw values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using HiPure Unviersal RNA Mini Kit(Magen).1.3 ug of total RNA was uesd for the construction of sequencing libraries.
Strand-specific libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: hippocampus


title: AS3h5


title: WT_rep1


title: genomic DNA from DLBCL.nonGC sample 60

source_name: DLBCL.nonGC sample 60


title: genomic DNA from DLBCL.nonGC sample 61

source_name: DLBCL.nonGC sample 61


title: genomic DNA from DLBCL.nonGC sample 59

source_name: DLBCL.nonGC sample 59


title: genomic DNA from DLBCL.nonGC sample 58

source_name: DLBCL.nonGC sample 58


title: genomic DNA from DLBCL.nonGC sample 57

source_name: DLBCL.nonGC sample 57


title: Ribo-STAMP MDA-MB-231 48h CoCl2 Replicate 2

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Replicate 2 of MDA-MB-231 cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1)  expression vector induced for 48h with 48h CoCl2-induced hypoxia treatment.

data_processing:
Sequencing data was processed using the Isoseq v4 pipeline with lima (parameter: --isoseq) to generate full-length non-concatemer reads and isoseq refine (parameter: --require-polya) to generate refined reads.
HEK293T APOBEC1-only and Ribo-STAMP data were aligned to hg19 reference and MDA-MB-231 Ribo-STAMP data (NT and CoCl2) were aligned to hg38 reference using pbmm2 align (parameter: --preset ISOSEQ).
QC was completed using NanoPlot (parameters: --raw and --tsv_stats).
Reads were filtered for uniquely mapped reads and read counts obtained using IsoQuant (parameters: --data_type pacbio, --transcript_quantification unique_only, and --gene_quantification unique_only)
Edits were identified and filtered using custom scripts.
Assembly: hg19, hg38
Supplementary files format and content: tab-delimited file containing edited positions, the number of reads with C-to-U edits at each positions (conversion), the total number of reads at each position, and each edit's assignment to a gene and isoform (BED)

growth_protocol: HEK293T and MDA-MB-231 cells were cultured independently in DMEM + 10% FBS (Gibco) at 37 °C with 5% CO2.

extract_protocol:
RNA was isolated with TRIzol extraction (Fisher) and column purification using the Direct-zol Miniprep kit (Zymo Research) as per manufacturer instructions.
RNA-seq libraries for HEK293T cells expressing APOBEC1-only or Ribo-STAMP expression vectors were prepared using the PacBio Iso-seq Express protocol (101-763-800) and SMRTbell Express Template Kit 2.0 (100-938-900) as per manufacturer instructions. RNA-seq libraries for MDA-MB-231 cells expressing the Ribo-STAMP expression vector with and without cobalt (II) chloride treatment were preapred using the PacBio SMRTbell prep kit 3.0 (102-141-700) as per manufacturer instructions.

treatment_protocol: HEK293T cells were treated with 1ug/mL doxycycline to induce expression of APOBEC1-only or Ribo-STAMP expression vectors. MDA-MB-231 cells were treated with 48h 1ug/mL doxycycline to induce Ribo-STAMP expression and one set of samples were treated with 48h 100uM cobald (II) chloride (Sigma, 15862-1ML-F).

value: 48h dox, 48h CoCl2


title: Ribo-STAMP MDA-MB-231 48h CoCl2 Replicate 1

description: Replicate 1 of MDA-MB-231 cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1)  expression vector induced for 48h with 48h CoCl2-induced hypoxia treatment.


title: AS3h4


title: genomic DNA from DLBCL.nonGC sample 56

source_name: DLBCL.nonGC sample 56


title: AS3h3


title: Ribo-STAMP MDA-MB-231 NT Replicate 2

description: Replicate 2 of MDA-MB-231 cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1)  expression vector induced for 48h without treatment.

value: 48h dox


title: genomic DNA from DLBCL.nonGC sample 55

source_name: DLBCL.nonGC sample 55


title: AS3h2


title: Ribo-STAMP MDA-MB-231 NT Replicate 1

description: Replicate 1 of MDA-MB-231 cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1)  expression vector induced for 48h without treatment.


title: genomic DNA from DLBCL.nonGC sample 54

source_name: DLBCL.nonGC sample 54


title: genomic DNA from DLBCL.nonGC sample 53

source_name: DLBCL.nonGC sample 53


title: WT_rep2

source_name: yeast


title: Ribo-STAMP HEK293T Replicate 3

description: Replicate 3 of HEK293T cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1) expression vector induced for 72h.

value: 72h dox


title: AS3h1


title: genomic DNA from DLBCL.nonGC sample 51

source_name: DLBCL.nonGC sample 51


title: genomic DNA from DLBCL.nonGC sample 50

source_name: DLBCL.nonGC sample 50


title: NC6


title: Ribo-STAMP HEK293T Replicate 2

description: Replicate 2 of HEK293T cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1) expression vector induced for 72h.


title: genomic DNA from DLBCL.nonGC sample 48

source_name: DLBCL.nonGC sample 48


title: NC5


title: NC4


title: genomic DNA from DLBCL.nonGC sample 44

source_name: DLBCL.nonGC sample 44


title: genomic DNA from DLBCL.nonGC sample 42

source_name: DLBCL.nonGC sample 42


title: genomic DNA from DLBCL.nonGC sample 45

source_name: DLBCL.nonGC sample 45


title: NC3

source_name: hippocampus


title: genomic DNA from DLBCL.nonGC sample 43

source_name: DLBCL.nonGC sample 43


title: NC2


title: genomic DNA from DLBCL.nonGC sample 49

source_name: DLBCL.nonGC sample 49


title: genomic DNA from DLBCL.nonGC sample 52

source_name: DLBCL.nonGC sample 52


title: APOBEC1-only HEK293T Replicate 2

description: Replicate 2 of HEK293T cells with doxycycline-inducible APOBEC1-only expression vector induced for 72h.


title: genomic DNA from DLBCL.nonGC sample 41

source_name: DLBCL.nonGC sample 41


title: Ribo-STAMP HEK293T Replicate 1

description: Replicate 1 of HEK293T cells with doxycycline-inducible Ribo-STAMP (RPS2 fused to APOBEC1) expression vector induced for 72h.


title: NC1


title: genomic DNA from DLBCL.nonGC sample 40

source_name: DLBCL.nonGC sample 40


title: genomic DNA from DLBCL.nonGC sample 39

source_name: DLBCL.nonGC sample 39


title: Rat skin Afa, rep3

first: qing

last: you

address: 800 Dongchuan

institute: Shanghai Jiao Tong University

data_processing:
Raw sequences were mapped to the rat reference sequence by Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.16.1).
P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: Ensemble 96
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Back skins were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: afatinib


title: genomic DNA from DLBCL.nonGC sample 37

source_name: DLBCL.nonGC sample 37


title: genomic DNA from DLBCL.GC sample 36

source_name: DLBCL.GC sample 36


title: APOBEC1-only HEK293T Replicate 3

description: Replicate 3 of HEK293T cells with doxycycline-inducible APOBEC1-only expression vector induced for 72h.


title: Rat skin Afa, rep2


title: genomic DNA from DLBCL.nonGC sample 38

source_name: DLBCL.nonGC sample 38


title: KSHV_Enriched_BCBL-1_48h_induced_3KbPlus_BR1

description:
IsoSeq_CFLs_NC009333_mapped.read_ends.bedgraph.gz
IsoSeq_CFLs_NC009333_mapped.read_starts.bedgraph.gz

data_processing:
Library strategy: IsoSeq
Circular Consensus sequences (.ccs.bam) files for all samples were processed together by the IsoSeq pipeline to generate consensus full length (CFLs) reads from all samples.
CFLs were mapped to the KSHV reference genome (NCBI accession number NC_009333.1) using gmap tool for long read sequence alignment.
TRIMD end validator and TRIMD start validator scripts were run to produce bedgraph files of isoform 5' and 3' ends
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: BedGraph files of isoform 5' and 3' ends
Library strategy: Iso-Seq

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol.
Full-length cDNAs were prepared using Low Input RNA: cDNA Synthesis and Amplification kit (NEB, Catalog No. E6421) as per the manufacturer’s guidelines. Full-length cDNAs were hybridized with KSHV baits to capture the KSHV specific cDNAs for preapring KSHV-Enriched libraries. cDNAs were size-fractionated and re-amplified. SMRTbell library adapters were ligated to cDNA fractions for preparing PacBio SMRT-Seq libraries.

value: Primary effusion lymphoma cells

value: WT

value: Induced


title: genomic DNA from DLBCL.nonGC sample 47

source_name: DLBCL.nonGC sample 47


title: genomic DNA from DLBCL.nonGC sample 46

source_name: DLBCL.nonGC sample 46


title: genomic DNA from DLBCL.GC sample 35

source_name: DLBCL.GC sample 35


title: genomic DNA from DLBCL.GC sample 34

source_name: DLBCL.GC sample 34


title: Rat skin Afa, rep1


title: BCBL-1_48h_induced_3KbPlus


title: APOBEC1-only HEK293T Replicate1

description: Replicate 1 of HEK293T cells with doxycycline-inducible APOBEC1-only expression vector induced for 72h.


title: Rat skin Control, rep3

value: vehicle


title: genomic DNA from DLBCL.GC sample 33

source_name: DLBCL.GC sample 33


title: genomic DNA from DLBCL.GC sample 32

source_name: DLBCL.GC sample 32


title: KSHV_Enriched_BCBL-1_48h_induced_1.5-3Kb_BR1


title: genomic DNA from DLBCL.GC sample 30

source_name: DLBCL.GC sample 30


title: genomic DNA from DLBCL.GC sample 31

source_name: DLBCL.GC sample 31


title: Rat skin Control, rep1


title: Rat skin Control, rep2


title: KSHV_Enriched_BCBL-1_48h_induced_3KbPlus_BR2


title: genomic DNA from DLBCL.GC sample 27

source_name: DLBCL.GC sample 27


title: genomic DNA from DLBCL.GC sample 28

source_name: DLBCL.GC sample 28


title: KSHV_Enriched_BCBL-1_48h_induced_BR2


title: KSHV_Enriched_BCBL-1_48h_induced_1.5-3Kb_BR2


title: genomic DNA from DLBCL.GC sample 25

source_name: DLBCL.GC sample 25


title: KSHV_Enriched_BCBL-1_48h_induced_BR1


title: genomic DNA from DLBCL.GC sample 26

source_name: DLBCL.GC sample 26


title: BCBL-1_48h_induced_BR1


title: genomic DNA from DLBCL.GC sample 24

source_name: DLBCL.GC sample 24


title: genomic DNA from DLBCL.GC sample 22

source_name: DLBCL.GC sample 22


title: Adjacent normal colon tissue EVs, 39N, sEVs

city: Suita

first: Kentaro

last: Jingushi

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

description: RNA isolated from small EVs

data_processing:
CLC Genomics Workbench v9.5.3 (Qiagen)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork.
Trimmed sequence reads were mapped to UCSC hg19 using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: UCSC hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Adjacent normal colon tissue

extract_protocol:
RNA contained in EVs was isolated using the miRNeasy mini kit (QIAGEN, Hilden, Germany), following the manufacturer’s protocol. Small EVs (5 × 10^8 particles), large EVs (5 × 10^7 particles) were used to extract RNA.
RNA libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina (NEB) in accordance with the manufacturer’s instructions, and libraries were sequenced on the HiSeq 2500 platform (Illumina) in 75-base pair single-end reads.

value: Adjacent normal colon tissue

tag: vesicle type

value: Small EVs


title: Adjacent normal colon tissue EVs, 40N, sEVs

description: RNA isolated from small EVs


title: genomic DNA from DLBCL.GC sample 21

source_name: DLBCL.GC sample 21


title: Adjacent normal colon tissue EVs, 37N, sEVs

description: RNA isolated from small EVs


title: genomic DNA from DLBCL.GC sample 20

source_name: DLBCL.GC sample 20


title: genomic DNA from DLBCL.GC sample 29

source_name: DLBCL.GC sample 29


title: genomic DNA from DLBCL.GC sample 18

source_name: DLBCL.GC sample 18


title: Adjacent normal colon tissue EVs, 35N, sEVs

description: RNA isolated from small EVs


title: Cow 8 adipocytes, Insulin, 7 h

city: East Lansing

first: G. Andres

last: Contreras

state: MI

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

data_processing:
Data quality control was performed with FastQC v.0.11
clean reads were mapped to the bosTau7 reference genome using HISAT 2.1.0
Assembly: bosTau7
Supplementary files format and content: tab delimited .txt file

organism: Bos taurus

source_name: Right flank subcutaneous adipose tissue

growth_protocol: Adipocytes progenitors were harvest by outgrowth expansion. Cells were induced with a standard adipogenic cocktail (insulin, IBMX, PPARg agonist, corticoid) and manteined for 7 days.

extract_protocol:
RNA was extracted using the Maxwell®RSC simplyRNA cells kit (AS1390, Promega, Madison, WI)
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: Adipocytes were treated with Isoproterenol 1 µM, Lipopolysaccharide (LPS) 1 µg/mL, Insulin 1 µg/L, Insulin + LPS or no reagents (Basal) for 7 h

value: Right flank subcutaneous adipose tissue

value: Stromal Vascular Fraction Derived Preadipocytes

value: Cell media + Insulin  1ug/L


title: genomic DNA from DLBCL.GC sample 16

source_name: DLBCL.GC sample 16


title: genomic DNA from DLBCL.GC sample 19

source_name: DLBCL.GC sample 19


title: genomic DNA from DLBCL.GC sample 17

source_name: DLBCL.GC sample 17


title: Cow 8 adipocytes, Insulin +  Lipopolysaccharide, 7 h

value: Cell media + Insulin  1ug/L + LPS 1 ug/mL


title: Cow 8 adipocytes, Lipopolysaccharide, 7 h

value: Cell media + LPS 1 ug/mL


title: genomic DNA from DLBCL.GC sample 15

source_name: DLBCL.GC sample 15


title: Cow 8 adipocytes, Isoproterenol, 7 h

value: Cell media + Isoproterenol 1 uM


title: Adjacent normal colon tissue EVs, 30N, sEVs

description: RNA isolated from small EVs


title: genomic DNA from DLBCL.GC sample 13

source_name: DLBCL.GC sample 13


title: genomic DNA from DLBCL.GC sample 12

source_name: DLBCL.GC sample 12


title: genomic DNA from DLBCL.GC sample 23

source_name: DLBCL.GC sample 23


title: genomic DNA from DLBCL.GC sample 14

source_name: DLBCL.GC sample 14


title: Colon cancer EVs, 40T, sEVs

description: RNA isolated from small EVs

source_name: Colon cancer tissue

value: Colon cancer tissue


title: Cow 6 adipocytes, Insulin +  Lipopolysaccharide, 7 h


title: genomic DNA from DLBCL.GC sample 11

source_name: DLBCL.GC sample 11


title: Colon cancer EVs, 39T, sEVs

description: RNA isolated from small EVs


title: Cow 6 adipocytes, Insulin, 7 h


title: genomic DNA from DLBCL.GC sample 10

source_name: DLBCL.GC sample 10


title: genomic DNA from DLBCL.GC sample 08

source_name: DLBCL.GC sample 08


title: Cow 6 adipocytes, Lipopolysaccharide, 7 h


title: Adjacent normal colon tissue EVs, 34N, sEVs

description: RNA isolated from small EVs

source_name: Adjacent normal colon tissue


title: genomic DNA from DLBCL.GC sample 07

source_name: DLBCL.GC sample 07


title: genomic DNA from DLBCL.GC sample 05

source_name: DLBCL.GC sample 05


title: genomic DNA from DLBCL.GC sample 06

source_name: DLBCL.GC sample 06


title: Colon cancer EVs, 37T, sEVs

description: RNA isolated from small EVs


title: Cow 6 adipocytes, Isoproterenol, 7 h

source_name: Right flank subcutaneous adipose tissue


title: Colon cancer EVs, 34T, sEVs

description: RNA isolated from small EVs


title: Cow 6 adipocytes, basal, 7h

value: Cell media


title: genomic DNA from DLBCL.GC sample 04

source_name: DLBCL.GC sample 04


title: genomic DNA from DLBCL.GC sample 03

source_name: DLBCL.GC sample 03


title: BCBL-1_48h_induced_BR2


title: Colon cancer EVs, 30T, sEVs

description: RNA isolated from small EVs


title: Colon cancer EVs, 35T, sEVs

description: RNA isolated from small EVs


title: genomic DNA from DLBCL.GC sample 09

source_name: DLBCL.GC sample 09


title: genomic DNA from DLBCL.GC sample 02

source_name: DLBCL.GC sample 02


title: WK-521-dFCS_Periphery_5dpi_2

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Sequenced reads were trimmed with fastp (v.0.21.0).
Sequenced reads were mapped to the golden hamster, SARS-CoV-2, and BANAL-20-236 reference genomes using STAR (v.2.6.1c).
Assembly: Golden hamster (GCF_017639785.1), BANAL-20-236 (MZ937003.2), and SARS-CoV-2 (NC_045512.2)
Supplementary files format and content: Expression read count matrix of hamster lung hila and peripheries (out_featureCount_matrix.txt)

organism: Mesocricetus auratus

source_name: lung periphery

extract_protocol:
Total RNA was extracted using QIAamp RNA Blood Mini Kit (Qiagen, Cat# 52304)
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

value: lung periphery

tag: infection

value: WK-521 dFCS

tag: time


title: genomic DNA from t.DLBCL sample 88

source_name: t.DLBCL sample 88

tag: entity


title: Cow 5 adipocytes, Insulin +  Lipopolysaccharide, 7 h


title: WK-521-dFCS_Periphery_5dpi_1


title: genomic DNA from DLBCL.GC sample 01

source_name: DLBCL.GC sample 01


title: WK-521-dFCS_Periphery_5dpi_4


title: Adjacent normal colon tissue EVs, 40N, LEVs

description: RNA isolated from large EVs

value: Large EVs


title: Cow 5 adipocytes, Insulin, 7 h


title: Adjacent normal colon tissue EVs, 39N, LEVs

description: RNA isolated from large EVs


title: WK-521_Periphery_5dpi_4


title: Cow 5 adipocytes, Lipopolysaccharide, 7 h


title: Adjacent normal colon tissue EVs, 37N, LEVs

description: RNA isolated from large EVs


title: WK-521_Periphery_5dpi_3


title: WK-521_Periphery_5dpi_2


title: BANAL-20-236_Periphery_5dpi_4


title: Cow 5 adipocytes, basal, 7h


title: Adjacent normal colon tissue EVs, 34N, LEVs

description: RNA isolated from large EVs


title: Cow 8 adipocytes, basal, 7h


title: WK-521-dFCS_Periphery_5dpi_3


title: BANAL-20-236_Periphery_5dpi_3


title: BANAL-20-236_Periphery_5dpi_2


title: WK-521_Periphery_5dpi_1


title: Adjacent normal colon tissue EVs, 35N, LEVs

description: RNA isolated from large EVs


title: BANAL-20-236_Periphery_5dpi_1


title: KU-cHCC-005 cells, Vehicle (DPBS), 24h

city: Seoul

first: Jayoung

last: Lee

address: 120, Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea

country: South Korea

institute: Konkuk University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to Dog10K Boxer Tasha whole genome using Tophat
FPKM calculation using Cufflink
Assembly: Dog10K Boxer Tasha
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

organism: Canis lupus familiaris

growth_protocol: KU-cHCC-001, KU-cHCC-002, KU-cHCC-004, KU-cHCC-005 cells were cultured in Advanced DMEM supplemented with 10% FBS, 1X Glutamax (Gibco), 1X ZellSheild (Minerva Biolabs), 10mM HEPES (Sigma-Aldrich) and 0.4mM N-acetyl-L-cysteine (Sigma-Aldrich) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: 8*10^5 cells were seeded in a 6-well plate. After 24h, the cells were treated with the vehicle control or the drugs (15 μm toceranib or 30 μm sorafenib) for 24 h and harvested.

value: Primary cultured canine HCC cell line

value: DPBS


title: KU-cHCC-005 cells, Sorafenib-treated (30μM), 24h

value: Soraefnib 30μM


title: Adjacent normal colon tissue EVs, 30N, LEVs

description: RNA isolated from large EVs


title: Colon cancer EVs, 40T, LEVs

description: RNA isolated from large EVs


title: Saline_Periphery_5dpi_2

value: Mock-infected


title: Saline_Periphery_5dpi_1


title: Colon cancer EVs, 39T, LEVs

description: RNA isolated from large EVs


title: Colon cancer EVs, 37T, LEVs

description: RNA isolated from large EVs


title: WK-521-dFCS_Periphery_2dpi_4


title: WK-521-dFCS_Periphery_2dpi_2


title: Cow 5 adipocytes, Isoproterenol, 7 h


title: KU-cHCC-005 cells, Toceranib-treated (15μM), 24h

value: Toceranib 15μM


title: WK-521-dFCS_Periphery_2dpi_3


title: KU-cHCC-004 cells, Toceranib-treated (15μM), 24h


title: WK-521-dFCS_Periphery_2dpi_1


title: Colon cancer EVs, 34T, LEVs

description: RNA isolated from large EVs


title: Colon cancer EVs, 35T, LEVs

description: RNA isolated from large EVs


title: KU-cHCC-004 cells, Vehicle (DPBS), 24h


title: Saline_Periphery_5dpi_3


title: KU-cHCC-004 cells, Sorafenib-treated (30μM), 24h


title: WK-521_Periphery_2dpi_2


title: KU-cHCC-004 cells, Vehicle (DMSO), 24h

value: DMSO


title: Saline_Periphery_5dpi_4


title: Colon cancer EVs, 30T, LEVs

description: RNA isolated from large EVs


title: WK-521_Periphery_2dpi_3


title: WK-521_Periphery_2dpi_1


title: KU-cHCC-005 cells, Vehicle (DMSO), 24h


title: KU-cHCC-002 cells, Toceranib-treated (15μM), 24h


title: BANAL-20-236_Periphery_2dpi_4


title: KU-cHCC-002 cells, Vehicle (DPBS), 24h


title: BANAL-20-236_Periphery_2dpi_3


title: KU-cHCC-002 cells, Sorafenib-treated (30μM), 24h


title: WK-521-dFCS_Hilum_5dpi_3

source_name: lung hilum

value: lung hilum


title: BANAL-20-236_Periphery_2dpi_1


title: G2_1

city: lanzhou

first: bai

last: jun

institute: Lanzhou University Second Hospital

data_processing:
1.mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data；2. mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database；3.mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: hg38
Supplementary files format and content: gene_count_matrix.csv

extract_protocol:
RNA was harvrsted useing TRIzol Reagent.1.94 ug of total RNA was used for the construction of sequencing libraries.
Constructing a transcriptome library using PolyA enrichment standard library kit

value: human myeloid leukemia cell line

value: K562/IM cell, Lycorine


title: BANAL-20-236_Periphery_2dpi_2


title: G2_2


title: G2_3


title: WK-521-dFCS_Hilum_5dpi_4


title: WK-521-dFCS_Hilum_5dpi_2


title: G4_3

value: K562/IM cell, Control


title: WK-521_Periphery_2dpi_4


title: KU-cHCC-002 cells, Vehicle (DMSO), 24h


title: WK-521-dFCS_Hilum_5dpi_1


title: G4_2


title: WK-521_Hilum_5dpi_3


title: WK-521_Hilum_5dpi_4


title: G4_1


title: WK-521_Hilum_5dpi_1


title: KU-cHCC-001 cells, Vehicle (DPBS), 24h


title: WK-521_Hilum_5dpi_2


title: G3_3

value: Lycorine treat


title: BANAL-20-236_Hilum_5dpi_3


title: G3_2


title: BANAL-20-236_Hilum_5dpi_4


title: KU-cHCC-001 cells, Sorafenib-treated (30μM), 24h


title: KU-cHCC-001 cells, Vehicle (DMSO), 24h


title: BANAL-20-236_Hilum_5dpi_1


title: BANAL-20-236_Hilum_5dpi_2


title: G3_1


title: G1_3

value: Control


title: Saline_Hilum_5dpi_4


title: Saline_Hilum_5dpi_2


title: Saline_Hilum_5dpi_3


title: KU-cHCC-001 cells, Toceranib-treated (15μM), 24h


title: G1_2


title: BM, scRNAseq

city: Xiamen

first: Qiuyue

last: Long

state: Fujian

address: Xiang‘an east Road 2000

institute: Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University

description: 10x genomics

data_processing:
The raw gene expression matrix generated from each sample were aggregated using CellRanger (v5.0.1) provided on the 10x genomics website. Downstream analysis was done using the R package Seurat (v 3.2.0). Quality control was applied to cells based on number of detected genes and proportion of mitochondrial reads per cell. Specifically, cells with less than 200 detected genes or cells with >90% of the proportion of the maximum genes were filtered out.  For the mitochondrial metric, sorted the cells in descending order of mitochondrial read ratio, and filtered out the top 15% of cells. Potential doublets were identified and removed by DoubletDetection.Cell cycle analysis was performed by using CellCycleScoring function in Seurat program. The gene expression dataset was normalized, subsequent principal component analysis was conducted using only the 2000 highly variable genes in the dataset.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
The 6-9 week old C57BL/6J mice were endotracheally innoculated Klebsiella pneumoniae (ATCC 43816) to induce sepsis. PBMCs and BMMCs were separated with the 1.084 g/mL Ficoll medium. In brief, EDTA-anticoagulated whole blood and BM single-cell suspension diluted with an equal volume phosphate-buffered saline (PBS), spread flat on the surface of Ficoll layer and centrifugated at 350 g for 30 min. Next, the middle PBMC and BMMC layer was retained and erythrocytes in it was lysed using lysis solution at room temperature for 5min. After lysis terminating and cell washing with precooled PBS adding 2% fetal bovine serum, cell counting and viability were assessed using trypan blue by microscopy. Finally, once ensuring that the cell viability exceeded 88%, isolated PBMCs and PBMCs were frozen in liquid nitrogen until use.
Prepared single-cell suspension is partitioned into GEMs (Gel Beads in Emulsions) in the automated Chromium Controller, and then mRNAs are reverse transcribed into cDNAs. Library was performed according to the manufacture's instruction (single cell 3' v2 protocol, 10× Genomics).

value: Bone marrow

value: BMMC

value: immune cell in BM

value: no treatment


title: Saline_Hilum_5dpi_1


title: G1_1


title: PB, scRNAseq

description: 10x genomics

source_name: Peripheral blood

value: Peripheral blood

value: PBMC

value: immune cell in PB


title: WK-521-dFCS_Hilum_2dpi_4

value: WK-521 dFCS


title: WK-521-dFCS_Hilum_2dpi_3


title: RNA, 1956

city: Saint Louis

first: Robert

middle: D

last: Schreiber

state: MO

address: 425 South Euclid

department: Department of Pathology and Immunology

institute: Washington University in St. Louis

description:
Mutation_1956.vcf
RNAseq_TPM_1956_F244.xlsx

data_processing:
For whole exome sequencing, paired-end 151 base pair reads were sequenced on the NovaSeq6000 to aim for 100x coverage in normal and 250x in tumor samples. For RNA-seq, paired-end 151 base pair reads were generated on the NovaSeq6000 to generate for a minimum of 80 million reads per sample; reads were aligned to the mouse genome reference sequence build GRCm38. Alignment was performed using a custom in-house pipeline and the splice-aware aligner STAR (RRID_SCR_004463). The Salmon tool (RRID:SCR_017036) was  used to quantify transcript abundance from the tumor RNA-seq reads generated.
Assembly: mm9
Supplementary files format and content: Tab-delimited text file contains mutation data
Supplementary files format and content: Excel file contains TPM values for F244 and 1956 lines

source_name: In vitro cultured cells

extract_protocol:
DNA and RNA were isolated from in vitro cultured 1956 and F244 cells using QIAamp DNA Kits (Qiagen, Cat# 56304) and RNeasy Kits (Qiagen, Cat# 74104), respectively, according to manufacturer’s instructions. DNA was isolated from tails of female C57BL/6N and male 129S6 mice to serve as control for 1956 and F244, respectively.
Exome sequencing libraries were generated using the NEBNext Ultra II FS Kit (NEB, Cat# E7805). Tumor RNA was subjected to DNase treatment and ribodepletion prior to library construction using NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB, Cat# E7760).

value: In vitro cultured cells


title: 48 h Induced BCBL-1 deepCAGE Seq

data_processing:
Illumina 1.9 basecalling
Alignment to the KSHV genome (NCBI accession number NC_009333.1) using STAR version 2.7.0b with default parameters
Generation of bedgraph coverage files using bamCoverage tool by deepTools suite
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Signal coverage files for the KSHV genome in bedgraph format

extract_protocol:
TRIzol reagent (Ambion)
nAnT-iCAGE

value: Primary effusion lymphoma cells

value: WT

value: Induced


title: WK-521-dFCS_Hilum_2dpi_2

value: lung hilum


title: MAC-T cells, IL10Rα knockout, MAP infection, rep3 (KO-MAP_15)

city: Guelph

first: Christine

middle: Francoise

last: Baes

state: Ontario

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

data_processing:
CLC Genomics Workbench software 20.0.4 (QIAGEN, Aarhus, Denmark)
The sequence data were trimmed for adaptor sequence, low-quality sequence (Phred score >30) using CLC genomic benchwork (parameter- Quality limit: 0.05 and max 2 ambiguous nucleotides)
The trimmed pair-end sequence reads were mapped to the bovine reference genome (ARS-UCD1.2) using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.6 similarity fraction: 0.6)
Differentially expressed (DE) genes analyses for "MAC-T cells, wildtype, no infection" versus "MAC-T cells, wildtype, MAP infection", "MAC-T cells, wildtype, no infection" versus "MAC-T cells, IL10Rα knockout, no infection", "MAC-T cells, wildtype, MAP infection" versus "MAC-T cells, IL10Rα knockout, MAP infection", and "MAC-T cells, IL10Rα knockout, no infection" versus "MAC-T cells, IL10Rα knockout, MAP infection" contrasts were performed
Gene expression levels were quantified in reads per kilobase per million mapped reads (RPKM) and transformed to log 2 were performed using CLC genomic benchwork
DE genes between each contrast were defined by a p-value ≤0.01, FDR ≤0.05, and |fold change|≥2.
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Common delimited text files.  Chromosome, start and end physical position, fold change, p-value, FDR p-value correction, gene, Ensemble ID, and RPKM (reads per kilobase of transcript, per million mapped reads) for each of the samples being included in the contrast.

source_name: mammary epithelium

growth_protocol:
MAC-T wild type and IL10RA KO cell line were cultured in T25 tissue culture flasks (Corning, Tewksbury, MA, USA) at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen, Burlington, ON, Canada) supplemented with 4.0 mM L-glutamine, 10% heat inactivated fetal bovine serum (FBS; Invitrogen), 25 mM HEPES buffer (Invitrogen), 0.25 μg/ml amphotericin B (Invitrogen), 1% Penicillin/Streptomycin (100 unit/ml of Penicillin and 100 μg/ml Streptomycin; Invitrogen), 1 mM Sodium Pyruvate (Invitrogen), and 5 μg/ml insulin-transferrin-selenium (Invitrogen).
Mycobacterium avium subsp. Paratuberculosis (MAP) was cultured in Middlebrook 7H9 broth (Sigma-Aldrich) supplemented with 10% oleic acid, albumin, dextrose, catalase (OADC; Becton, Dickinson, Canada), 0.05% Tween 80 (Sigma-Aldrich), and 2 mg/L mycobactin J (Allied Monitor Inc., Fayette, MO). The bacterial culture was incubated at 37°C and 5% CO2.

extract_protocol:
Total RNA extraction was carried out using the RNeasy mini kit (Qiagen, Germany) from both uninfected and MAP-infected samples according to the manufacturer’s protocol. The DNA traces were removed by DNase I treatment (Fermentas, Waltham, MA, USA). The concentration and purity of the RNA samples were determined at A260/280 nm ratios using the Cytation-5 Spectrophotometer. The integrity of the RNA samples was assessed using Bioanalyzer. The samples with higher than 7 RNA Integrity Number (RIN) were chosen for RNA Seq.
RNA-seq, including library construction were outsourced to Genewiz, Azenta Life Sciences, US

treatment_protocol: The IL10RA KO and Wild type MAC-T cells were seeded at 1.2 x10^5 cells per well in separate 24-well plates and incubated overnight at 37°C and 5% CO2 to reach 80% confluence. Both cell types were either infected with MAP or provided an equivalent volume of MAP-carrier solution media (uninfected control) for 72 h. Bacterial CFU were determined using the pellet wet-weight method, whereby 1 mg of MAP Madonna pellet was equal to 10^7 CFU. MAP was added to each cell type to achieve a 10:1 multiplicity of infection and then spun for 2 min at 250x g to ensure MAP interaction with the cells.

value: mammary epithelium

value: IL10R{alpha} knockout

value: MAP infection


title: WK-521-dFCS_Hilum_2dpi_1


title: DNA, Control for 1956

data_processing:
For whole exome sequencing, paired-end 151 base pair reads were sequenced on the NovaSeq6000 to aim for 100x coverage in normal and 250x in tumor samples. For RNA-seq, paired-end 151 base pair reads were generated on the NovaSeq6000 to generate for a minimum of 80 million reads per sample; reads were aligned to the mouse genome reference sequence build GRCm38. Alignment was performed using a custom in-house pipeline and the splice-aware aligner STAR (RRID_SCR_004463). The Salmon tool (RRID:SCR_017036) was  used to quantify transcript abundance from the tumor RNA-seq reads generated.
Assembly: mm9
Supplementary files format and content: Tab-delimited text file contains mutation data
Supplementary files format and content: Excel file contains TPM values for F244 and 1956 lines
Library strategy: Whole exome sequencing

source_name: tail

value: tail


title: MAC-T cells, IL10Rα knockout, MAP infection, rep4 (KO-MAP_16)


title: MAC-T cells, IL10Rα knockout, MAP infection, rep2 (KO-MAP_14)


title: RNA, F244

description:
Mutation_F244.vcf
RNAseq_TPM_1956_F244.xlsx


title: DNA, Control for F244


title: MAC-T cells, IL10Rα knockout, MAP infection, rep1 (KO-MAP_13)


title: DNA, 1956 cells


title: WK-521_Hilum_2dpi_4


title: WK-521_Hilum_2dpi_3